The phase, "Nice guys finish last" get chucked out completely, when it comes to anime that have a romantic focus. I've notice this emphasis of the male protagonist being that super nice and pretty much indistinguishable from the next guy in another anime.
Overly nice guys tend to end up with a harem following him and the only reason they are attracted to him is he happened to be kind to them one time. It is pretty predicable and I end up becoming underwhelmed with the males character and any romance that develops, tends to be flat.
Off the top of my head I've got two males that fit the bill, Teiichi from Tasogare Otome x Amnesia and Takeru from Maken-Ki. Teiichi, as I said in my review, he wasn't much of a character, but rather a storytelling device and he so happen to be nice to Yuuko, which become a pretty generic romance. Also Takeru is a guy who doesn't even want females to fight, even if pretty much all of them in the series is stronger than him physically and he has at least 3 girl in love with him.
The two animes themselves are very different, mainly Tasogare Otome was actually good, but you can see that the main attribute to these character is the fact that they are nice. Also, the main reason for the females being attracted to them is that males were nice to them.
However, nice guys aren't always something I frown at, they just need to be well developed character that don't stand out only because of their niceness toward the opposite sex. Just as an example, we have Takumi, all these 't' starting names, from Kaichou wa Maid-Sama, who I can say isn't always the generic nice guy, he has his more mischievous side.
In general I would say you can have a guy be nice in an anime, but at some point he need to present some other characteristic that makes for a well rounded character, maybe even a reason for him becoming that nice guy.